It's not FlashFXP specific. IglooFTP, SmartFTP and CuteFTP Pro all handle it the same way, which means one of the two ftp servers is misconfigured and does not fully support fxp the way FlashFXP expects it.
The only thing that bothers me is that FlashFXP detects that the transfer is finished (226 Transfer OK), but waits for something else ... perhaps you could FlashFXP simply wait for 226 Transfer OK and nothing else.
-Lars
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